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LimeSoDa: A dataset collection for benchmarking of machine learning regressors in digital soil mapping
Get PDFDigital soil mapping (DSM) relies on a broad pool of statistical methods, yet determining the optimal method for a given context remains challenging and contentious. Benchmarking studies on multiple datasets are needed to reveal strengths and limitations of commonly used methods. Existing DSM studies usually rely on a single dataset with restricted access, leading to incomplete and potentially misleading conclusions. To address these issues, we introduce an open-access dataset collection called Precision Liming Soil Datasets (LimeSoDa). LimeSoDa consists of 31 field-and farm-scale datasets from various countries. Each dataset has three target soil properties: (1) soil organic matter or soil organic carbon, (2) clay content and (3) pH, alongside a set of features. Features are dataset-specific and were obtained by optical spectroscopy, proximal-and remote soil sensing. All datasets were aligned to a tabular format and are ready-to-use for modeling. We demonstrated the use of LimeSoDa for benchmarking by comparing the predictive performance of four learning algorithms across all datasets. This comparison included multiple linear regression (MLR), support vector regression (SVR), categorical boosting (CatBoost) and random forest (RF). The results showed that although no single algorithm was universally superior, certain algorithms performed better in specific contexts. MLR and SVR performed better on high-dimensional spectral datasets, likely due to better compatibility with principal components. In contrast, Cat-Boost and RF exhibited considerably better performances when applied to datasets with a moderate number (<20) of features. These benchmarking results illustrate that the performance of statistical methods can be highly context-dependent. LimeSoDa therefore provides an important resource for improving the development and evaluation of statistical methods in DSM
Long-term recovery and food web response of benthic macrofauna following cessation of bottom trawling in a marine protected area
Get PDFThe understanding of the depletion of species and communities and recovery following the reduction of pressures is fundamental in conservation biology. The impact of bottom trawl fisheries on benthic communities has been well studied, but there are few studies of the long-term recovery after the cessation of bottom trawling. Here we followed the recovery of the benthic macrofaunal community over 12 years in a large (426 km(2)) no-take zone (NTZ) area in the south Kattegat after demersal trawling was stopped and compared it to a nearby area where trawling continued. Using multivariate analyses, we found shifts in the community composition. Two species of burrowing brittle stars, Amphiura filiformis and Amphiura chiajei, dominated abundance and biomass and decreased in the closed area (abundance effect size A. filiformis 48%; A. chiajei 45%). In parallel, there was an increase in benthivore flatfish. Stomach contents of the dominating flatfishes matched the availability of benthic prey taxa, and brittle stars were the staple food. Food web effects thus appear to override the decrease in mortality of the dominant macrofauna caused by the cessation of trawling in the NTZ. The recovery response in the species community in the NTZ correlated with the pattern in community composition along a chronic bottom trawling intensity gradient in the same area. This indicates that the recovery of the benthic community is not random but follows a successional pattern that can also be observed in chronic states of disturbance from bottom trawling. This is important information from the perspective of management efforts to restore marine ecosystems from the impact of bottom trawl fisheries, as it indicates that reduced effort may lead to predictable recovery
Therapeutic Value of Lactobacillus gasseri 345A in Chronic Constipation
Get PDFBackgroundChronic constipation is a prevalent, burdensome gastrointestinal disorder whose etiology and pathophysiology remain poorly understood. Differences in the composition of the intestinal microbiota have been shown between constipated patients and healthy people. Data indicate that these microbial differences contribute to the disorder. MethodsPreclinical studies in mice examined the effects of Lactobacillus gasseri on intestinal motility ex vivo, the reversal of motility inhibition by mu-opioid receptor agonists ex vivo and in vivo in mice, and the effects on capsaicin-stimulated transient receptor potential vanilloid 1 (TRPV1) in Jurkat cells. Thereafter, a clinical study of 40 women with functional constipation was conducted to investigate the effects of Lactobacillus gasseri with a randomized parallel design. After 14 days of baseline recording, treatment with Lactobacillus gasseri or placebo was given over 28 days, with 14 days of follow-up. Outcomes with complete spontaneous bowel movements (CSBM), spontaneous bowel movements, emptying frequency, abdominal pain, time spent for defecation, Bristol stool form scale, use of rescue laxatives, and impact on sex life were investigated. Key ResultsIn preclinical studies, Lactobacillus gasseri increased intestinal motility in an ex vivo model, reversed the motility inhibition caused by mu-opioid receptor agonist ex vivo and in vivo in mice, and counteracted capsaicin-stimulated activity of TRPV1 in Jurkat cells. In the clinical trial, Lactobacillus gasseri showed a significant reduction in abdominal pain, along with a correlation and tendency for an increased number of CSBM. Few adverse events were encountered. Conclusions and InferencesTreatment with Lactobacillus gasseri can alleviate pain sensations in functional constipation, possibly with an improved bowel-emptying function
Evidence of Holarctic distribution: common frog Rana temporaria eggs in Fennoscandia host photosymbiotic green algae (Oophila sp.)
Get PDFSymbiosis is a commonly occurring phenomenon, with most plants and animals being holobionts, comprising of a host and its corresponding symbionts. It is, however, less common to have a symbiont only under a specific life stage and even more so between a photosynthesizing organism and a vertebrate animal. One such relationship is found between the unicellular green algae Oophila amblystomatis and the North American yellow-spotted salamander Ambystoma maculatum, which is so far the only known endosymbiotic relationship between an alga and a vertebrate. In this study we investigate the possible occurrence of O. amblystomatis in Fennoscandian egg clutches from the genus Rana using citizen science data. We establish that egg capsules of the common frog Rana temporaria in Sweden act as a host species for two subclades of the monophyletic genus Oophila on a microgeographical scale (< 10 km) using a phylogenetic analysis. Furthermore, we investigated a possible endosymbiotic relationship between O. amblystomatis and R. temporaria embryos with fluorescence microscopy, which showed no algal invasion of frog tissue or cells in vivo. The association with a known symbiont Oophila may hold ecological importance for ontogeny, individual fitness, behavior, population dynamics and evolutionary potential of R. temporaria. However, the reciprocal benefits to both partners have not been determined for any Oophila-bearing ranid. We discuss the possible Holarctic distribution of Oophila and consider the implications of the relationship between R. temporaria and O. amblystomatis
PFAS contamination in key indian states: A critical review of environmental impacts, regulatory challenges and predictive exposure
Get PDFPer-and polyfluoroalkyl substances (PFAS) have emerged as major global environmental contaminants due to their persistence, bioaccumulation and toxicity potential. PFAS pollution is growing in India, particularly in industrial regions with limited environmental monitoring. This critical review focuses on PFAS sources, environmental fate, and transport across key Indian states, emphasizing environmental and human health risks, including drinking water exposure. A predictive model was developed to assess PFAS contamination over 30 years (2024-2054), revealing a strong positive correlation (r = 0.95, p <0.001) between initial contamination levels and projected PFAS concentrations in surface water matrices, with some states anticipated to exceed safe limits. Human exposure estimation through fish consumption highlighted elevated PFAS exposure in states with high fish consumption rates, such as West Bengal and Tamil Nadu. Cumulative daily intake (CDI) analysis demonstrated substantial long-term exposure risks, incorporating water and dietary source contributions. The findings reveal critical challenges such as regulatory gaps, inadequate monitoring, and technological barriers that hinder India's ability to address PFAS contamination effectively. Comparing guideline limits globally, including those of the United States and European Union, India's regulatory framework remains in its early stages, underscoring the need for systematic monitoring and robust remediation strategies. A systematic gap analysis underscores the need for enhanced research on PFAS source tracing near industrial and urban centres. The findings emphasize the urgency of implementing stronger regulations, expanding monitoring systems, increasing public and stakeholder awareness, and informed policymaking to mitigate the growing threat of PFAS contamination in India
Sensitivity analysis of the Green Shoulder indices in pre-emergence detection of single trees attacked by European spruce bark beetle
Get PDFThe application of hyperspectral cameras for forest health monitoring enables precise detection of stress-related changes in vegetation, such as those caused by spruce bark beetle infestations. In a previous study, Green Shoulder Indices (GSIs) were proposed, which exhibited high capacities to indicate trees with decreasing vitality caused by spruce bark beetle infestation using hyperspectral drone images. However, the detection accuracy of these indices may be influenced by the selection of various parameters. This study conducts a sensitivity analysis of the indices and aims to assess how the detection accuracy is impacted by different parameter choices. The detectability obtained from the GSIs was calculated and compared when (1) using the brightest or centremost pixels from the crown segments with different thresholds, (2) smoothing the spectral curves with different levels, and (3) using bands with varying bandwidths. The results showed that the GSIs were not sensitive to whether the brightest or centremost pixels were used for detection. Stronger smoothing caused the derivative peak at 545 nm to shift towards smaller wavelengths when a tree was under increasing stress, but the detectability obtained using GSIs did not decrease with stronger smoothing. The simplified GSIs using three wide spectral bands centred at 490 nm, 530 nm, and 550 nm (MS GSIs) slightly decreased the detection accuracy compared to narrowband MS GSIs, but the differences were minor, e.g. decreased from 0.86 to 0.80 using the index with the highest detectability (delta GSCR1(MS)). This study highlights the robustness of GSIs against tested factors and implies their potential for forest stress monitoring and damage control
High-quality draft genome sequences of seven Ralstonia spp. isolated from temperate forest soils
Get PDFWe report seven highquality draft genomes of Ralstonia spp. isolated from the Harvard Forest Long-Term Warming Experimental plots: four de novo hybrid assemblies and three de novo long-read assemblies. The genomes have a minimum estimated completeness of 92.6% and an average GC content of 63.45%
Biochemical and functional properties of vesicles from planktonic and biofilm phenotypes of Limosilactobacillus reuteri DSM 17938
Get PDFLimosilactobacillus reuteri DSM 17938 is among the world's most studied probiotic strains and has been shown to provide several health benefits for the host. We have previously shown that the cell-free supernatant of L. reuteri DSM 17938 possesses antimicrobial activity and contains several bioactive compounds. Furthermore, the strain was shown to be a biofilm producer that releases both planktonic and biofilm Membrane Vesicles (MVs). In this study, membrane vesicles isolated from planktonic (pMVs) and biofilm (bMVs) phenotypes were comparatively investigated for their toxicity, ability to kill cancer as well as non-cancer cell lines and modulate phagocytosis in murine macrophages. Neither pMVs nor bMVs showed any in vivo toxicity in a Galleria mellonella model, and weakly affected cancer and noncancerous cell viability after both short- and long-term treatments. However, they were able to affect phagocytosis in lipopolysaccharide challenged RAW 264.7 macrophages, suggesting possible immunomodulatory properties. NMR-based metabolomic analysis of pMVs and bMVs identified and quantified engulfed compounds, mainly organic acids and amino acids, with lactate being the most abundant molecule in both vesicle types. bMVs contained higher concentrations of all measured metabolites compared to pMVs. Proteomic analysis of pMVs and bMVs described equivalent protein cargos, emphasizing quantitative compositional differences that presumably reflect the physiological state of each parent bacterial phenotype. Through the assignment of molecules possibly acting as mediators of immune/inflammatory responses in the host and/or modulating known beneficial effects of L. reuteri, important signaling functions of these vesicles were suggested. Finally, storage stability of MVs up to four weeks was established
Resultat från övervakningen av kustfisk : Asköfjärden (Egentliga Östersjön) 2005–2024
Get PDFI den här rapporten redovisas resultaten från provfisket i Asköfjärden. Provfisket är en del av den regionala miljöövervakningen för kustfisk och har utförts i augusti varje år sedan 2005. Provfisket utförs med Nordiska kustöversiksnät, och fångstens artsammansättning, samt fiskens storlek och antal studeras. I samband med provfisket noteras även omgivningsvariabler. Åldersbestämning av abborre utförs efter genomfört provfiske. Provfiskeområdet ligger i Trosa kommun i Södermanlands län, och kustvattentypen är Mellankustvatten i Östergötlands och Stockholms skärgård. Området är relativt djupt och exponerat, samt innehåller få lek- och uppväxtområden för typiska varmvattenarter. Till skillnad från flera närliggande provfiskeområden anses Asköfjärden vara obetydligt påverkad av lokal mänsklig aktivitet. De vanligaste arterna i fångsten är abborre och mört, som tillsammans utgjort drygt 58 % av den totala fångsten. Totalfångsten per nät och natt har ökat sedan provfiskets start och kan till stor del förklaras av ökad förekomst av skarpsill och strömming. Området har genomgått en förändring i åldersfördelning för abborre – med en större andel unga individer i näten. De abborrar som fångas i fisket är dessutom vid bättre kondition och längre vid samma ålder än de var vid samma längd i början i av tidsserien. De allt större antalet svartmunnad smörbult som påträffas i provfisket skulle kunna indikera att arten blir allt vanligare i området
Alternative strategies based on transgenic Drosophila melanogaster for the functional characterization of insect Ionotropic Receptors
Get PDFBackgroundInsect Ionotropic Receptors (IRs) are a relatively uncharted territory. Some studies have documented IR activation by recording neuronal activity in situ, others by their heterologous expression in Xenopus oocytes or mis-expressing IRs from Drosophila melanogaster or from the related D. sechellia into the D. melanogaster "ionotropic receptor decoder" neuron, which lacks the endogenous tuning receptor subunit but expresses IR-coreceptors.ResultsIn this study, we first made use of Drosophila olfactory sensory neurons (OSNs) different from the "ionotropic receptor decoder", demonstrating that by replacing or introducing IRs alongside the native D. melanogaster ones, functional heteromeric complexes can be formed. IR41a1 from the lepidopteran Cydia pomonella exhibits binding to polyamines and the IR75d from the dipteran Drosophila suzukii binds hexanoic acid. Secondly, expressing D. suzukii's putative acid sensor IR64a into the "ionotropic receptor decoder" of D. melanogaster inhibits the response to the main activators of neighboring neurons from the same sensillum, despite that IR64a does not respond to acids. In situ hybridization on the antennae of D. suzukii unveils wide expression of IR64a in neurons proximal to the sacculus. Structural modeling analysis does not explain its absence of binding to acids; conversely, this approach identifies key amino acids features explaining the binding of hexanoic acid by IR75d. Finally, we have also explored alternative methods to heterologously express IRs based on Human Embryonic Kidney cells (HEK293). Despite observing correct expression of IRs in transfected cells through immunohistochemistry experiments, this approach did not achieve successful deorphanization of these receptors.ConclusionOur findings highlight the potential use of Drosophila OSNs as a valuable tool for functional characterization of IRs from different insect species: for the first time, we have provided evidence of IR-functionalities within alternative OSNs from the Drosophila's "ionotropic receptor decoder" neuron to functionally characterize and deorphanize IRs from lineages that are evolutionarily distant from the D. melanogaster subgroup, contributing to the understanding of chemosensory modalities in D. suzukii and C. pomonella, two globally significant agricultural pests. Additionally, the unsuccessful deorphanization in HEK cells highlights the complex requirements for IR functionality, supporting the use of Drosophila OSNs as a more suitable expression system